Bungle the Glass Cat, an inveterate explorer of the Land of Oz, reports witnessing an unusual sight: a group of strange beings who dance under a full moon, then retreat to an underground passage. Dorothy, accompanied by Bungle and Flicker, goes to investigate, as an ambassador from Ozma. (Flicker is a character introduced by Shanower in The Ice King of Oz, one of his five Oz graphic novels. Flicker is a diminutive wax man with a flame in place of a head of hair.) Flicker dislikes Bungle for her vanity and boasting; Dorothy works to keep peace between them.

Dorothy and her companions find their way into a subterranean world called Ma-dul-ma-dun, ruled by Queen Piopelp. Her people are sapient and sentient mushrooms — though they are dreary and enervated excuses for living beings. Their world, lit by blue-green phosphorescence, is dazzlingly beautiful, with soaring architecture and intricate carving — but emotionally it is cold and dismal.

Dorothy and Flicker receive a hostile welcome, though Piopelp falls in love with Bungle, re-christens her "Beloved," and longs to keep her forever. In the end, Flicker and Bungle must tolerate each other and co-operate to rescue Dorothy from imprisonment and death.

Shanower's story bears a relationship with Glinda of Oz, L. Frank Baum's final Oz book. Piopelp and Ma-dul-ma-dun compare with Coo-ee-oh and the submersible city of the Skeezers. In both cases, a dictatorial queen rules a subsurface domain of technical accomplishment and great beauty, but a place of repression and capricious tyranny. "Mushroom Queen" also bears resemblances to Shanower's other subterranean mushroom people story, Trot of Oz, his collaboration with Glenn Ingersoll.